There are a couple things that must be kept in mind when discussing the 49ers’ 32nd-ranked passing game.

First, the 49ers have constructed an offense that is rooted in the run game. Their personnel and their philosophy are ground-oriented. The first thing most people ask when the 49ers lose is, “Why didn’t Frank Gore run the ball more?”

General manager Trent Baalke believes the way to sustain success is to be able to run the football (even when other teams know you’re going to run it) and stop the run on defense.

And that seems to be a reasonable approach, considering the 49ers have made it to the NFL’s final four the past two seasons and were beaten by like-minded teams both times.

Second, the 49ers are 6-3. And they’re in good position to again advance to the playoffs.

But the problems in the passing game understandably became a focus after a 10-9 loss to the Carolina Panthers on Sunday because: a) They lost the game and failed to score a touchdown; b) Quarterback Colin Kaepernick threw for a career-low 91 yards, and the 49ers’ offense managed a paltry 46 yards of passing offense.

Yes, the Panthers have a very good defense. They’re ranked No. 2 in the NFL. But, still, those numbers are “unacceptable,” in the words of wide receiver Anquan Boldin.

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There’s plenty of blame to go around, for sure. And here’s a look at what went wrong against the Panthers and who’s to blame:

Colin Kaepernick: He gets assigned the most blame because, really, it all starts and stops with the quarterback. Kaepernick is regarded as a franchise quarterback, and he’s still in line for a big contract extension from the 49ers at the end of the season.

So it’s his responsibility to take what’s given to him and make it work. And there’s no doubt a player with such phenomenal physical gifts can make this work.

Last season, Kaepernick was mostly a one-read quarterback. But most of the time his one read was Michael Crabtree, with whom he built a lot of trust. Kaepernick delivered the ball on rhythm and was not shy about giving Crabtree opportunities to make plays. Oftentimes, Crabtree rewarded Kaepernick’s confidence with catches, yards and touchdowns.

This season, Kaepernick has not had Crabtree as his preferred weapon. In comparing this season to last season on Wednesday, Kaepernick seemingly alluded to that missing element of the passing game.

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“I don’t think you can really compare it,” Kaepernick said. “There’s different components this year and last year, so it’s comparing apples and oranges.”

On Sunday, Kaepernick certainly was not smooth about going through his progression. And, a lot of times, he has not been decisive with his first read, either.

One example was a second-and-7 situation from the Carolina 27 early in the second quarter. Mario Manningham was the primary receiver on the left side, and he was open as he made his break. The pocket was clean. But Kaepernick held onto the ball too long and made a late throw on the run that Manningham failed to catch at the sideline. The play was a lot more difficult than it had to be. It should’ve been a first down completion. Instead, the 49ers ended up settling for a field goal.

Greg Roman/Jim Harbaugh: Offensive coordinator Greg Roman and coach Jim Harbaugh need to be better at giving Kaepernick an easier second read when he does not deliver a throw to the primary target. In the first quarter, Anquan Boldin was wide open against the cornerback on a post pattern, but the linebacker slid over to close that window. Kaepernick did not pull the trigger. He looked to Manningham on the other side. Manningham was wide open, but Manningham had not come out of his break, yet. There was no simple bail-out plan, and Kaepernick was sacked.

The 49ers’ game plan should also include a variety of pass plays designed to get the ball out of Kaepernick’s hands quickly with swing passes and screens. The 49ers need to mix it up, calling some designed quick passes on early downs. During training camp, Kaepernick proved he has that club in his bag as one day he lofted nicely placed screen passes to Frank Gore and LaMichael James.

Kaepernick’s strength is driving the ball down the field, but those plays would work better if a steady diet of short passes are also called to keep defenses off balance.

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Pass protection:

Despite surrendering six sacks for minus-45 yards, the 49ers’ pass protection was good for most of the day. Generally, Kaepernick was able to get to the depth on his drops and get rid of the ball. But problems occurred when he held onto the ball or moved unnecessarily out of the pocket.

There were a couple plays on which right tackle Anthony Davis was beaten and Kaepernick had no chance. In the fourth quarter, left guard Mike Iupati surrendered a pressure that blew up a play. But on two occasions, the Panthers recorded sacks when they came free unblocked on delayed blitzes. The offensive line excels in the running game, but it also provided Kaepernick with enough protection on Sunday to have a good day.

Wide receivers/tight ends: The most overrated storyline in the woes of the passing game is the perceived inability of the pass targets to get open. In watching the all-22 game video, this does not seem like much of a problem at all. The receivers are getting open – but that, obviously, has not translated into much production.

The big play that got away in Sunday’s game was tight end Vance McDonald’s inability to hang onto a perfectly thrown pass from Kaepernick in the fourth quarter. It would’ve been about a 40-yard gain deep into Panthers territory. It’s a safe bet the 49ers would’ve come out of that possession with at least a field goal.

McDonald had both hands on the ball, but Carolina linebacker Luke Kuechly grabbed McDonald’s left arm after the pass arrived to break it up. That’s a ball McDonald should have caught.

And it also demonstrates how everything must be working in order for a play to succeed. Kaepernick did his job with his read and throw. The coaches designed a good play and called it at an opportune time. And the pass protection gave Kaepernick all the time he needed.

And if that pass had been completed, the 49ers probably would’ve won the game and there would not be such an uproar over the team’s 32nd-ranked passing game.